Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007779.1 Corchorus capsularis cultivar CVL-1 contig07800, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61469
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:957 original size:333 final size:333
Alignment explanation
Indices: 314--1973 Score: 1829
Period size: 335 Copynumber: 4.9 Consensus size: 333
304 TCCTCAATCG
* * *
314 AAATTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAATGCGTTCCGGTGCCCC
1 AAATTTTAACCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCC
* * * * *
379 GACTTAGTTTTGCATGATTTTTTGCGCCATGACTGCTTTAAATTTCTATATTAATCTTACCAAAT
66 GACTCAGTTTTGCATGATTTTTGGCGCCATGACTCCTTTAAATATCTATATTCATCTTACCAAAT
* * *
444 CTCATCCGCAATGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAATCCG
131 CTCAGCCACAATGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAATCAG
* *
509 AAATTAATTTTAAAAAAATAGGAAAAACGGTATTTGAAGCGTGAAATACCCTTCAATC-TTTTTG
196 AAATTAATTTTAAAAAAATAGGAAAAACGATATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTG
* *
573 TATTGAATTATATATTTCTTATGAGTATTGGGGCATAGAATTGAGGGAAAAAAATTTCTGGGTCA
261 TATTGAATTATATATTTCTTATGAGTATTGTGGCAAAGAATTGAGGGAAAAAAATTTC-GGGTCA
*
638 TTTTTTTCA
325 TTTTTTGCA
* * *
647 AAATTTTAACCGAAATAATGTACTAACCATCACGGTTTTTTGCTAAAAACGCTTTCTGGGGCCCC
1 AAATTTTAACCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCC
* * *
712 GACTCAGTTTTGCATGATTTTTTGCGCCATGACTCCTTTAAATTTCTATATTCATCGTACCAAAT
66 GACTCAGTTTTGCATGATTTTTGGCGCCATGACTCCTTTAAATATCTATATTCATCTTACCAAAT
* ** * *
777 CTCATCTGCAATGGATTTAAGGATACACTTTTATGAAGATCTGAAAATTGTTTCGATTTAATCAG
131 CTCAGCCACAATGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAATCAG
* * *
842 AAATTAATTTTTAAAAAATATGAAAAACGGTATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTG
196 AAATTAATTTTAAAAAAATAGGAAAAACGATATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTG
* *
907 TATTGAATTATATATTTCTTAAGAGTATTGAGGCAAAGAATTGA-GGAAAAAAATTTCGGGTCAT
261 TATTGAATTATATATTTCTTATGAGTATTGTGGCAAAGAATTGAGGGAAAAAAATTTCGGGTCAT
971 TTTTTGCA
326 TTTTTGCA
* *
979 AAATTTTAATCGAAATCATGTACTAAAACCATCACGGTTTTTTTGCTAAAAACGCGTTCCGGGTC
1 AAATTTTAACCGAAATCATGTACT--AACCATCACGG-TTTTTTGCTAAAAACGCGTTCCGGGGC
* * * * *
1044 CCAGACTCAGTTTTGCATGATTTTTGGCGCTGA-GACTCCTTGAAATATATATATTCGTCTTACC
63 CCCGACTCAGTTTTGCATGATTTTTGGCGC-CATGACTCCTTTAAATATCTATATTCATCTTACC
* *
1108 AAATCTCAGCCACATTGGATTTAAGGATACATTTTTACGAGGATCTGAAAATTGTTTCGATTTAA
127 AAATCTCAGCCACAATGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAA
* * * * * *
1173 TTAGAAATTAA-TTTGAAAAAATAGGAAAAACGATATTTGAAACGTGAAAAACTCGTCAATTTTT
192 TCAGAAATTAATTTTAAAAAAATAGGAAAAACGATATTTGAAGCGTGAAAAACCCTTCAATCTTT
* * * * *
1237 TTTATATTGAATTATATATTTCTTGTGAGTATTGTGGCAAAAAATTGA-GAAAAAAAAATTCGGG
257 TTTGTATTGAATTATATATTTCTTATGAGTATTGTGGCAAAGAATTGAGGGAAAAAAATTTCGGG
1301 TCATTTTTTGCA
322 TCATTTTTTGCA
* * * * * * * *
1313 AAATTTTAACCGAAATCTTGTACAAACCTTCATGGTTTTTTGCTAAGAACACGTTCCGGGGTCCT
1 AAATTTTAACCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCC
* * * * * * * *
1378 GACTCAATTTTGCAAGATTTTTGGTGTCAAGACTCCTTCAAATATCTATATTTATCTTATCAAAT
66 GACTCAGTTTTGCATGATTTTTGGCGCCATGACTCCTTTAAATATCTATATTCATCTTACCAAAT
* * * **
1443 CTTAGCCACATTGGATTTAAGGGTATC-TTTTTACG-AGCATCTGAATCTTGTTTCGATTTAATC
131 CTCAGCCACAATGGATTTAAGGATA-CATTTTTACGAAG-ATCTGAAAATTGTTTCGATTTAATC
* ** * *
1506 AAAAATT-ATTTTGAGAAAAAAAATAGGAAAAACGATATAAGAAGCGTGAAAAGCCCTTCAATAT
194 AGAAATTAATTTT----AAAAAAATAGGAAAAACGATATTTGAAGCGTGAAAAACCCTTCAATCT
* ** ** * *
1570 TCTTTGCGTTGAATTATATATTTCTTATGACCATTGTGGCCATA-AATTGAGGGAAAAAAA-AT-
255 TTTTTGTATTGAATTATATATTTCTTATGAGTATTGTGG-CAAAGAATTGAGGGAAAAAAATTTC
* * *
1632 GTGTCAATTTTCTGTA
319 GGGTC-ATTTTTTGCA
* * * * * * *
1648 AAATTTTAACTGAAATCGTATACTAATCATCACGGTTTTTTTTGCTAAAAACGCATTTCGGGGGC
1 AAATTTTAACCGAAATCATGTACTAACCATCACGG--TTTTTTGCTAAAAACGCGTTCCGGGGCC
* *** * * * * * * *
1713 CCGTCTCAGTTTCATATGATTTTGGGCATCCA-AAATCCTTGAAATATCTATATCCATCTTAACA
64 CCGACTCAGTTTTGCATGATTTTTGGC-GCCATGACTCCTTTAAATATCTATATTCATCTTACCA
** * * ** * **
1777 AATCTCAATCATATTGGATTTAAGGATATGTTTTTAC-AACCATCTGAATCTTGTTTCGATTTAA
128 AATCTCAGCCACAATGGATTTAAGGATACATTTTTACGAA-GATCTGAAAATTGTTTCGATTTAA
* * * *** *
1841 TCAGAAATCAATTTGGGAGAAAAAAAAGAATCAGGAAAAACCATATTTTTGGCGTGAAAAGCCCT
192 TCAGAAATTAATTT-------TAAAAA-AAT-AGGAAAAACGATATTTGAAGCGTGAAAAACCCT
* * * * *
1906 TCAATTTTTTTTATATTGAATTATATATTTTTTATGAGTATTATGGCTAAA-AATTGA-GAAAAA
248 TCAATCTTTTTTGTATTGAATTATATATTTCTTATGAGTATTGTGGC-AAAGAATTGAGGGAAAA
1969 AAATT
312 AAATT
1974 CGATATCCAT
Statistics
Matches: 1132, Mismatches: 161, Indels: 58
0.84 0.12 0.04
Matches are distributed among these distances:
330 3 0.00
331 140 0.12
332 46 0.04
333 249 0.22
334 198 0.17
335 261 0.23
336 12 0.01
337 128 0.11
338 6 0.01
341 5 0.00
342 12 0.01
343 72 0.06
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (333 bp):
AAATTTTAACCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCC
GACTCAGTTTTGCATGATTTTTGGCGCCATGACTCCTTTAAATATCTATATTCATCTTACCAAAT
CTCAGCCACAATGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAATCAG
AAATTAATTTTAAAAAAATAGGAAAAACGATATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTG
TATTGAATTATATATTTCTTATGAGTATTGTGGCAAAGAATTGAGGGAAAAAAATTTCGGGTCAT
TTTTTGCA
Found at i:1690 original size:668 final size:662
Alignment explanation
Indices: 314--1975 Score: 1883
Period size: 668 Copynumber: 2.5 Consensus size: 662
304 TCCTCAATCG
* * *
314 AAATTTTAACCGAAATCGTGTACTAACCATCACGG-TTTTTTGCTAAAAATGCGTTCCGGTGCCC
1 AAATTTTAACTGAAATCGTGTACTAACCATCACGGTTTTTTTGCTAAAAACGCGTTCCGG-GTCC
* * * * * *
378 CGACTTAGTTTTGCATGATTTTTTGCGC-CATGACTGCTTTAAATTTCTATATTAATCTTACCAA
65 CGACTCAGTTTTGCATGATTTTTGGCGCTCA-GACTCCTTGAAATATCTATATTCATCTTACCAA
* * *
442 ATCTCATCCGCAATGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAATC
129 ATCTCAACCACATTGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAATC
* * * * *
507 CGAAATTAATTTTAAAAAAATAGGAAAAACGGTATTTGAAGCGTGAAATACCCTTCAA-TCTTTT
194 AGAAATTAA-TTTGAAAAAATAGGAAAAACGATATTTGAAGCGTGAAAAACCCTTCAATTTTTTT
* * * * *
571 TGTATTGAATTATATATTTCTTATGAGTATTGGGGCATAGAATTGAGGGAAAAAAATTTCTGGGT
258 TATATTGAATTATATATTTCTTATGAGTATTGTGGCAAAAAATTGA--GAAAAAAAATTC-GGGT
* * * *
636 CATTTTTTTCAAAATTTTAACCGAAATAATGTACTAACCATCACGGTTTTTTGCTAAAAACGCTT
320 CATTTTTTGCAAAATTTTAACCGAAATAATGTACAAACCATCACGGTTTTTTGCTAAAAACACGT
* * * * * * *
701 TCTGGGGCCCCGACTCAGTTTTGCATGATTTTTTGCGCCATGACTCCTTTAAATTTCTATATTCA
385 TCCGGGGCCCCGACTCAATTTTGCAAGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCA
* ** *
766 TCGTACCAAATCTCATCTGCAATGGATTTAAGGATACACTTTTATGAAGATCTGAAAATTGTTTC
450 TCGTACCAAATCTCAGCCACAATGGATTTAAGGATACACTTTTACGAAGATCTGAAAATTGTTTC
* * * * **
831 GATTTAATCAGAAATTAATTTTTAAAAAATATGAAAAACGGTATTTGAAGCGTGAAAAACCCTTC
515 GATTTAATCAAAAATTAATTTTAAAAAAATAGGAAAAACGATATAAGAAGCGTGAAAAACCCTTC
* * * **
896 AATCTTTTTTGTATTGAATTATATATTTCTTAAGAGTATTGAGGCAAAGAATTGAGGAAAAAAAT
580 AATATTCTTTGCATTGAATTATATATTTCTTAAGACCATTGAGGCAAAGAATTGAGGAAAAAAAT
* *
961 TTCGGGTCATTTTTTGCA
645 ATCGGGTCATTTTCTGCA
*
979 AAATTTTAA-TCGAAATCATGTACTAAAACCATCACGGTTTTTTTGCTAAAAACGCGTTCCGGGT
1 AAATTTTAACT-GAAATCGTGTACT--AACCATCACGGTTTTTTTGCTAAAAACGCGTTCCGGGT
* * *
1043 CCCAGACTCAGTTTTGCATGATTTTTGGCGCTGAGACTCCTTGAAATATATATATTCGTCTTACC
63 CCC-GACTCAGTTTTGCATGATTTTTGGCGCTCAGACTCCTTGAAATATCTATATTCATCTTACC
* *
1108 AAATCTCAGCCACATTGGATTTAAGGATACATTTTTACGAGGATCTGAAAATTGTTTCGATTTAA
127 AAATCTCAACCACATTGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAA
* * * *
1173 TTAGAAATTAATTTGAAAAAATAGGAAAAACGATATTTGAAACGTGAAAAACTCGTCAATTTTTT
192 TCAGAAATTAATTTGAAAAAATAGGAAAAACGATATTTGAAGCGTGAAAAACCCTTCAATTTTTT
*
1238 TTATATTGAATTATATATTTCTTGTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAATTCGGGTC
257 TTATATTGAATTATATATTTCTTATGAGTATTGTGGCAAAAAATTGAG-AAAAAAAATTCGGGTC
** * * *
1303 ATTTTTTGCAAAATTTTAACCGAAATCTTGTACAAACCTTCATGGTTTTTTGCTAAGAACACGTT
321 ATTTTTTGCAAAATTTTAACCGAAATAATGTACAAACCATCACGGTTTTTTGCTAAAAACACGTT
* * * * *
1368 CCGGGGTCCTGACTCAATTTTGCAAGATTTTTGGTGTCAAGACTCCTTCAAATATCTATATTTAT
386 CCGGGGCCCCGACTCAATTTTGCAAGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCAT
* * * * * * **
1433 CTTATCAAATCTTAGCCACATTGGATTTAAGGGTATC-TTTTTACG-AGCATCTGAATCTTGTTT
451 CGTACCAAATCTCAGCCACAATGGATTTAAGGATA-CACTTTTACGAAG-ATCTGAAAATTGTTT
*
1496 CGATTTAATCAAAAATT-ATTTTGAGAAAAAAAATAGGAAAAACGATATAAGAAGCGTGAAAAGC
514 CGATTTAATCAAAAATTAATTTT----AAAAAAATAGGAAAAACGATATAAGAAGCGTGAAAAAC
* * * *
1560 CCTTCAATATTCTTTGCGTTGAATTATATATTTCTTATGACCATTGTGGCCATA-AATTGAGGGA
575 CCTTCAATATTCTTTGCATTGAATTATATATTTCTTAAGACCATTGAGG-CAAAGAATTGA-GGA
* *
1624 AAAAAA-AT-GTGTCAATTTTCTGTA
638 AAAAAATATCGGGTC-ATTTTCTGCA
* * * * *
1648 AAATTTTAACTGAAATCGTATACTAATCATCACGGTTTTTTTTGCTAAAAACGCATTTCGGGGGC
1 AAATTTTAACTGAAATCGTGTACTAACCATCACGG-TTTTTTTGCTAAAAACGC-GTTCCGGGTC
* *** * * * *
1713 CCGTCTCAGTTTCATATGA-TTTTGG-GCATCCAAAATCCTTGAAATATCTATATCCATCTTAAC
64 CCGACTCAGTTTTGCATGATTTTTGGCGC-T-CAGACTCCTTGAAATATCTATATTCATCTTACC
* * ** * **
1776 AAATCTCAATCATATTGGATTTAAGGATATGTTTTTAC-AACCATCTGAATCTTGTTTCGATTTA
127 AAATCTCAACCACATTGGATTTAAGGATACATTTTTACGAA-GATCTGAAAATTGTTTCGATTTA
* * *** *
1840 ATCAGAAATCAATTTGGGAGAAAAAAAAGAATCAGGAAAAACCATATTTTTGGCGTGAAAAGCCC
191 ATCAGAAATTAATTT----G----AAAA-AAT-AGGAAAAACGATATTTGAAGCGTGAAAAACCC
* * *
1905 TTCAATTTTTTTTATATTGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGAAAAAA
246 TTCAATTTTTTTTATATTGAATTATATATTTCTTATGAGTATTGTGGCAAAAAATTGAGAAAAAA
1970 AATTCG
311 AATTCG
1976 ATATCCATGT
Statistics
Matches: 839, Mismatches: 125, Indels: 54
0.82 0.12 0.05
Matches are distributed among these distances:
665 28 0.03
666 179 0.21
667 86 0.10
668 316 0.38
669 118 0.14
670 13 0.02
672 1 0.00
676 4 0.00
677 15 0.02
678 79 0.09
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (662 bp):
AAATTTTAACTGAAATCGTGTACTAACCATCACGGTTTTTTTGCTAAAAACGCGTTCCGGGTCCC
GACTCAGTTTTGCATGATTTTTGGCGCTCAGACTCCTTGAAATATCTATATTCATCTTACCAAAT
CTCAACCACATTGGATTTAAGGATACATTTTTACGAAGATCTGAAAATTGTTTCGATTTAATCAG
AAATTAATTTGAAAAAATAGGAAAAACGATATTTGAAGCGTGAAAAACCCTTCAATTTTTTTTAT
ATTGAATTATATATTTCTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTCGGGTCATTTT
TTGCAAAATTTTAACCGAAATAATGTACAAACCATCACGGTTTTTTGCTAAAAACACGTTCCGGG
GCCCCGACTCAATTTTGCAAGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCGTAC
CAAATCTCAGCCACAATGGATTTAAGGATACACTTTTACGAAGATCTGAAAATTGTTTCGATTTA
ATCAAAAATTAATTTTAAAAAAATAGGAAAAACGATATAAGAAGCGTGAAAAACCCTTCAATATT
CTTTGCATTGAATTATATATTTCTTAAGACCATTGAGGCAAAGAATTGAGGAAAAAAATATCGGG
TCATTTTCTGCA
Found at i:2070 original size:50 final size:50
Alignment explanation
Indices: 1995--2095 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
1985 TTGATCTATA
1995 GAAATATGTTATATCTGATCTTTGGTAATCAAGAAGCTATGTATATATGT
1 GAAATATGTTATATCTGATCTTTGGTAATCAAGAAGCTATGTATATATGT
2045 GAAATATGTTATATCTGATCTTTGGTAATCAAGAAGCTATGTATATATGT
1 GAAATATGTTATATCTGATCTTTGGTAATCAAGAAGCTATGTATATATGT
2095 G
1 G
2096 GCAGGCATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.40
Consensus pattern (50 bp):
GAAATATGTTATATCTGATCTTTGGTAATCAAGAAGCTATGTATATATGT
Found at i:2431 original size:15 final size:15
Alignment explanation
Indices: 2411--2440 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2401 TTTAAAGAAT
2411 TTGCAGCTATGCAAA
1 TTGCAGCTATGCAAA
2426 TTGCAGCTATGCAAA
1 TTGCAGCTATGCAAA
2441 CGTCAATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
TTGCAGCTATGCAAA
Found at i:6478 original size:21 final size:21
Alignment explanation
Indices: 6449--6489 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6439 CTCTATGGCC
*
6449 TCCCTCAATCGCTC-CTCCGCA
1 TCCCGCAATCGC-CGCTCCGCA
6470 TCCCGCAATCGCCGCTCCGC
1 TCCCGCAATCGCCGCTCCGC
6490 CTCCGCGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.12, C:0.54, G:0.15, T:0.20
Consensus pattern (21 bp):
TCCCGCAATCGCCGCTCCGCA
Found at i:16517 original size:2 final size:2
Alignment explanation
Indices: 16510--16536 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16500 TCAATCATAC
16510 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
16537 TGTCCGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19863 original size:29 final size:30
Alignment explanation
Indices: 19831--19891 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
19821 GAAAAGACCA
*
19831 ATATCCATTC-ACCAAAACCGAAAACAAGT
1 ATATCCATTCTACCAAAACAGAAAACAAGT
***
19860 ATATTTGTTCTACCAAAACAGAAAACAAGT
1 ATATCCATTCTACCAAAACAGAAAACAAGT
19890 AT
1 AT
19892 GTTGACATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (30 bp):
ATATCCATTCTACCAAAACAGAAAACAAGT
Found at i:21856 original size:6 final size:6
Alignment explanation
Indices: 21839--21872 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
21829 AGGATAAATA
* *
21839 AAAAAG ACAAAG ATAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
21873 CGAGGGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:25991 original size:9 final size:9
Alignment explanation
Indices: 25977--26004 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
25967 ATATATATAA
25977 AAAAAAAAG
1 AAAAAAAAG
25986 AAAAAAAAG
1 AAAAAAAAG
25995 AAAAAAAAG
1 AAAAAAAAG
26004 A
1 A
26005 TGAGACTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:26357 original size:5 final size:5
Alignment explanation
Indices: 26347--26379 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
26337 ACCTAGCTAG
*
26347 TTTCT TTTCT TTTCT TTTCT TTTCT TTTGT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
26380 AATTGACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:33828 original size:12 final size:13
Alignment explanation
Indices: 33802--33834 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
33792 TAAATTAATT
33802 ACAAACTAAACAA
1 ACAAACTAAACAA
*
33815 ACAAA-TAAATAA
1 ACAAACTAAACAA
33827 ACAAACTA
1 ACAAACTA
33835 CTAAACTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (13 bp):
ACAAACTAAACAA
Found at i:44361 original size:13 final size:14
Alignment explanation
Indices: 44343--44375 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
44333 AAAGGGAAAT
*
44343 AGAAGAAGAGAGG-
1 AGAAGAAAAGAGGA
44356 AGAAGAAAAGAGGA
1 AGAAGAAAAGAGGA
44370 AGAAGA
1 AGAAGA
44376 GGAACAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAGAGGA
Found at i:44455 original size:18 final size:18
Alignment explanation
Indices: 44432--44467 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
44422 ACTGATGATT
44432 CAGATTCTGAATAAATTA
1 CAGATTCTGAATAAATTA
44450 CAGATTCTGAATAAATTA
1 CAGATTCTGAATAAATTA
44468 GGATAGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
CAGATTCTGAATAAATTA
Found at i:56974 original size:17 final size:16
Alignment explanation
Indices: 56952--56983 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
56942 GCTGTCGGGT
56952 GAAGGAAGAAAGAAAAA
1 GAAGGAAG-AAGAAAAA
56969 GAAGGAAGAAGAAAA
1 GAAGGAAGAAGAAAA
56984 GAAAGGGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
GAAGGAAGAAGAAAAA
Done.